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Nadine Seidel, Wilhelm Seichter,
Acta Crystallographica Section E Structure Reports Online, Volume 68; https://doi.org/10.1107/s1600536812004229

Abstract:
In the title compound, C14H8Br2N2O2, the molecular structure features intramolecular N—H...O [2.639 (2) Å and 130°] and N—H...Br [3.053 (2) Å and 114°] hydrogen bonding. Due to inversion symmetry, the asymmetric part of the unit cell consits of one half-molecule. In the crystal, inversion dimers linked by pairs of N—H...O [2.955 (2) Å and 135°] hydrogen bonds occur. The structure also features C=O...π [3.228 (2) Å] and Br...Br [3.569 (1) Å] contacts
Journal of Synchrotron Radiation, Volume 5, pp 980-982; https://doi.org/10.1107/s0909049597020232

Abstract:
Spontaneous X-ray parametric scattering from a diamond single crystal has been observed at the Photon Factory. The high perfection of the diamond single crystal and the small angular divergence of synchrotron radiation has enabled down-converted X-ray photon pairs to scatter into two small solid angles which satisfy the phase-matching condition. High-efficiency noise reduction was performed using avalanche photodiode detectors with good time resolution.
, T. C. Fan, F. Y. Lin, C. H. Chang, P. K. Tseng, S. Yeh, H. H. Chen
Journal of Synchrotron Radiation, Volume 5, pp 471-474; https://doi.org/10.1107/s0909049597013691

Abstract:
A three-orthogonal-Hall-probe assembly with an `on the fly' mapping method has been developed to characterize an elliptically polarizing undulator (EPU). The underlying design concept is that it can measure the three real field components without any field correction under a reliable and synchronization measurement method. Therefore, the relative central position shift, orthogonal angle and the planar Hall effect error between the three Hall probes should be calibrated and readjusted. Experimental results demonstrate that this method can yield an r.m.s. reproducibility of 10 G cm for the three field components and 2 G for the peak field strength. Under precision conditions this system can completely measure the three on-axis field components within 2 min for a 4 m-long EPU.
Oleg Chubar, Pascal Elleaume, Joel Chavanne
Journal of Synchrotron Radiation, Volume 5, pp 481-484; https://doi.org/10.1107/s0909049597013502

Abstract:
RADIA is a three-dimensional magnetostatics computer code optimized for the design of undulators and wigglers. It solves boundary magnetostatics problems with magnetized and current-carrying volumes using the boundary integral approach. The magnetized volumes can be arbitrary polyhedrons with non-linear (iron) or linear anisotropic (permanent magnet) characteristics. The current-carrying elements can be straight or curved blocks with rectangular cross sections. Boundary conditions are simulated by the technique of mirroring. Analytical formulae used for the computation of the field produced by a magnetized volume of a polyhedron shape are detailed. The RADIA code is written in object-oriented C++ and interfaced to Mathematica [Mathematica is a registered trademark of Wolfram Research, Inc.]. The code outperforms currently available finite-element packages with respect to the CPU time of the solver and accuracy of the field integral estimations. An application of the code to the case of a wedge-pole undulator is presented.
, Alexei A. Vagin, , , Eleanor J. Dodson
Acta Crystallographica Section D Biological Crystallography, Volume 55, pp 247-255; https://doi.org/10.1107/s090744499801405x

Abstract:
This paper gives the equations for the use of fast Fourier transformations in individual atomic anisotropic refinement. Restraints on bonded atoms, on the sphericity of each atom and between non-crystallographic symmetry related atoms are described. These have been implemented in the program REFMAC and its performance with several examples is analysed. All the tests show that anisotropic refinement not only reduces the R value and Rfree but also improves the fit to geometric targets, indicating that this parameterization is valuable for improving models derived from experimental data. The computer time taken is comparable to that for isotropic refinements.
Alexei A. Vaguine, ,
Acta Crystallographica Section D Biological Crystallography, Volume 55, pp 191-205; https://doi.org/10.1107/s0907444998006684

Abstract:
In this paper we present SFCHECK, a stand-alone software package that features a unified set of procedures for evaluating the structure-factor data obtained from X-ray diffraction experiments and for assessing the agreement of the atomic coordinates with these data. The evaluation is performed completely automatically, and produces a concise PostScript pictorial output similar to that of PROCHECK [Laskowski, MacArthur, Moss & Thornton (1993). J. Appl. Cryst. 26, 283-291], greatly facilitating visual inspection of the results. The required inputs are the structure-factor amplitudes and the atomic coordinates. Having those, the program summarizes relevant information on the deposited structure factors and evaluates their quality using criteria such as data completeness, structure-factor uncertainty and the optical resolution computed from the Patterson origin peak. The dependence of various parameters on the nominal resolution (d spacing) is also given. To evaluate the global agreement of the atomic model with the experimental data, the program recomputes the R factor, the correlation coefficient between observed and calculated structure-factor amplitudes and Rfree (when appropriate). In addition, it gives several estimates of the average error in the atomic coordinates. The local agreement between the model and the electron-density map is evaluated on a per-residue basis, considering separately the macromolecule backbone and side-chain atoms, as well as solvent atoms and heterogroups. Among the criteria are the normalized average atomic displacement, the local density correlation coefficient and the polymer chain connectivity. The possibility of computing these criteria using the omit-map procedure is also provided. The described software should be a valuable tool in monitoring the refinement procedure and in assessing structures deposited in databases.
Journal of Synchrotron Radiation, Volume 24, pp 1218-1225; https://doi.org/10.1107/s1600577517011201

Abstract:
Many published literature sources have described the histopathological characteristics of post-traumatic syringomyelia (PTS). However, three-dimensional (3D) visualization studies of PTS have been limited due to the lack of reliable 3D imaging techniques. In this study, the imaging efficiency of propagation-based synchrotron radiation microtomography (PB-SRµCT) was determined to detect the 3D morphology of the cavity and surrounding microvasculature network in a rat model of PTS. The rat model of PTS was established using the infinite horizon impactor to produce spinal cord injury (SCI), followed by a subarachnoid injection of kaolin to produce arachnoiditis. PB-SRµCT imaging and histological examination, as well as fluorescence staining, were conducted on the animals at the tenth week after SCI. The 3D morphology of the cystic cavity was vividly visualized using PB-SRµCT imaging. The quantitative parameters analyzed by PB-SRµCT, including the lesion and spared spinal cord tissue area, the minimum and maximum diameters in the cystic cavity, and cavity volume, were largely consistent with the results of the histological assessment. Moreover, the 3D morphology of the cavity and surrounding angioarchitecture could be simultaneously detected on the PB-SRµCT images. This study demonstrated that high-resolution PB-SRµCT could be used for the 3D visualization of trauma-induced spinal cord cavities and provides valuable quantitative data for cavity characterization. PB-SRµCT could be used as a reliable imaging technique and offers a novel platform for tracking cavity formation and morphological changes in an experimental animal model of PTS.
, , K. Lauer, , X. Huang, W. Xu, J. Zhou, D. Shu, Y. Hwu,
Journal of Synchrotron Radiation, Volume 24, pp 1113-1119; https://doi.org/10.1107/s1600577517011183

Abstract:
A hard X-ray scanning microscope installed at the Hard X-ray Nanoprobe beamline of the National Synchrotron Light Source II has been designed, constructed and commissioned. The microscope relies on a compact, high stiffness, low heat dissipation approach and utilizes two types of nanofocusing optics. It is capable of imaging with ∼15 nm × 15 nm spatial resolution using multilayer Laue lenses and 25 nm × 26 nm resolution using zone plates. Fluorescence, diffraction, absorption, differential phase contrast, ptychography and tomography are available as experimental techniques. The microscope is also equipped with a temperature regulation system which allows the temperature of a sample to be varied in the range between 90 K and 1000 K. The constructed instrument is open for general users and offers its capabilities to the material science, battery research and bioscience communities.
M. Colapietro, A. Domenicano, C. Marciante, G. Portalone
Acta Crystallographica Section A Foundations of Crystallography, Volume 37; https://doi.org/10.1107/S0108767381093628

IUCrJ, Volume 4, pp 769-777; https://doi.org/10.1107/s2052252517013124

Abstract:
Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers. The electron densities obtained from mixing times of 2 and 50 s show clear binding of chitotriose to the enzyme at a high level of detail. The success of this approach shows the potential for high-throughput drug screening and even structural enzymology on short timescales at bright synchrotron light sources.
G. B. Jameson, W. Bachmann, H. R. Oswald, E. Dubler
Acta Crystallographica Section A Foundations of Crystallography, Volume 37; https://doi.org/10.1107/S0108767381096888

Journal of Synchrotron Radiation, Volume 24, pp 1195-1208; https://doi.org/10.1107/s1600577517012000

Abstract:
X-ray gas attenuators are used in high-energy synchrotron beamlines as high-pass filters to reduce the incident power on downstream optical elements. The absorption of the X-ray beam ionizes and heats up the gas, creating plasma around the beam path and hence temperature and density gradients between the center and the walls of the attenuator vessel. The objective of this work is to demonstrate experimentally the generation of plasma by the X-ray beam and to investigate its spatial distribution by measuring some of its parameters, simultaneously with the X-ray power absorption. The gases used in this study were argon and krypton between 13 and 530 mbar. The distribution of the 2pexcited states of both gases was measured using optical emission spectroscopy, and the density of argon metastable atoms in the 1s5state was deduced using tunable laser absorption spectroscopy. The amount of power absorbed was measured using calorimetry and X-ray transmission. The results showed a plasma confined around the X-ray beam path, its size determined mainly by the spatial dimensions of the X-ray beam and not by the absorbed power or the gas pressure. In addition, the X-ray absorption showed a hot central region at a temperature varying between 400 and 1100 K, depending on the incident beam power and on the gas used. The results show that the plasma generated by the X-ray beam plays an essential role in the X-ray absorption. Therefore, plasma processes must be taken into account in the design and modeling of gas attenuators.
, Lucia Alianelli
Journal of Synchrotron Radiation, Volume 24, pp 1120-1136; https://doi.org/10.1107/s1600577517011808

Abstract:
The shapes of single lens surfaces capable of focusing divergent and collimated beams without aberration have already been calculated. However, nanofocusing compound refractive lenses (CRLs) require many consecutive lens surfaces. Here a theoretical example of an X-ray nanofocusing CRL with 48 consecutive surfaces is studied. The surfaces on the downstream end of this CRL accept X-rays that are already converging toward a focus, and refract them toward a new focal point that is closer to the surface. This case, so far missing from the literature, is treated here. The ideal surface for aberration-free focusing of a convergent incident beam is found by analytical computation and by ray tracing to be one sheet of a Cartesian oval. An `X-ray approximation' of the Cartesian oval is worked out for the case of small change in index of refraction across the lens surface. The paraxial approximation of this surface is described. These results will assist the development of large-aperture CRLs for nanofocusing.
Acta Crystallographica Section C Structural Chemistry, Volume 73, pp 880-884; https://doi.org/10.1107/s2053229617013250

Abstract:
Macrocyclic ligand systems with a variety of (different) donor sites oftentimes give rise to very exciting and unexpected multinuclear metal complexes. We report herein the structure of a trinuclear mixed imidazolylidene/imidazolium nickel N-heterocyclic carbene (NHC) complex, namely di-μ-chlorido-bis{μ-calix[2]imidazolium[2]imidazolylidene[2]pyrazolate}trinickel(II) tetrakis(hexafluoridophosphate) acetonitrile tetrasolvate, [Ni3(C24H24N12)2Cl2](PF6)4·4CH3CN or [Ni3(LMe)2Cl2](PF6)4·4CH3CN, that can be understood as a trapped reaction intermediate during the synthesis of the respective [Ni2LMe](PF6)2 product. The structure not only contains protonated next to deprotonated imidazole heterocycles, but also Ni2+ ions with fundamentally different coordination modes within one molecule. Two of the three metal atoms are coordinated in a square-pyramidal fashion by half a ligand molecule and one chloride ligand, whereas the third Ni2+ ion is bound octahedrally by four pyrazolate moieties and two chloride anions.
Acta Crystallographica Section C Structural Chemistry, Volume 73, pp 896-904; https://doi.org/10.1107/s2053229617013213

Abstract:
Since the discovery of electrochemically active LiFePO4, materials with tunnel and layered structures built up of transition metals and polyanions have become the subject of much research. A new quaternary arsenate, sodium calcium trinickel aluminium triarsenate, NaCa1–x Ni3–2x Al2x (AsO4)3 (x = 0.23), was synthesized using the flux method in air at 1023 K and its crystal structure was determined from single-crystal X-ray diffraction (XRD) data. This material was also characterized by qualitative energy-dispersive X-ray spectroscopy (EDS) analysis and IR spectroscopy. The crystal structure belongs to the α-CrPO4 type with the space group Imma. The structure is described as a three-dimensional framework built up of corner-edge-sharing NiO6, (Ni,Al)O6 and AsO4 polyhedra, with channels running along the [100] and [010] directions, in which the sodium and calcium cations are located. The proposed structural model has been validated by bond-valence-sum (BVS) and charge-distribution (CHARDI) tools. The sodium ionic conduction pathways in the anionic framework were investigated by means of the bond-valence site energy (BVSE) model, which predicted that the studied material will probably be a very poor Na+ ion conductor (bond-valence activation energy ∼7 eV).
Acta Crystallographica Section C Structural Chemistry, Volume 73, pp 889-895; https://doi.org/10.1107/s2053229617013675

Abstract:
The comprehensive description of the crystal structure of a novel 1:1 cocrystal of 3,4,5-trifluorophenylboronic acid with urea, C6H4BF3O2·CH4N2O, is presented. Both components are good candidates for crystal engineering as they can create a variety of supramolecular synthons. The preference for the formation of different hetrosynthons is verified based on theoretical calculations. The synanti conformation of boronic acid has been found to be the most favourable in the formation of intermolecular interactions with urea. Moreover, the distortions present in the boron coordination sphere have been described quantitatively based on experimental data according to bond-valence vector model calculations. The results revealed that the deformation of the sphere is typical for a synanti conformation of boronic acids. The supramolecular structure of the cocrystal is composed of large synthons in the form of layers made up of O—H...O and N—H...O hydrogen bonds. The layers are joined via N—H...F hydrogen bonds which are unusual for urea cocrystal structures.
Yang Lu, Wei-Qiang Liao, Xiu-Ni Hua
Acta Crystallographica Section C Structural Chemistry, Volume 73, pp 885-888; https://doi.org/10.1107/s2053229617013614

Abstract:
As part of an exploration of new coordination polymers, a cadmium-dicyanamide complex, namely poly[benzyltriethylammonium [tri-μ-dicyanamido-κ6N1:N5-cadmium(II)]], {(C13H22N)[Cd(C2N3)3]} n , has been synthesized by the reaction of benzyltriethylammonium bromide, cadmium nitrate tetrahydrate and sodium dicyanamide in aqueous solution, and characterized by single-crystal X-ray diffraction at room temperature. In the crystal structure, each CdII cation is coordinated by six nitrile N atoms from six anionic dicyanamide (dca) ligands to furnish a slightly distorted octahedral geometry. Neighbouring CdII cations are linked by dicyanamide bridges to construct a two-dimensional anionic layer coordination polymer. One amide N atom in the bridging dca ligand is disordered over two sites. The cations lie between the anionic frameworks and there are no hydrogen-bond interactions between the cations and anions. The organic cations are not involved in the formation of the supramolecular network.
Acta Crystallographica Section C Structural Chemistry, Volume 73, pp 874-879; https://doi.org/10.1107/s2053229617013663

Abstract:
Halogen bonding (XB) is a highly-directional class of intermolecular interactions that has been used as a powerful tool to drive the design of crystals in the solid phase. To date, the majority of XB donors have been iodine-containing compounds, with many fewer involving brominated analogues. We report the formation of adducts in the vapour phase from a series of dibromoperfluoroalkyl compounds, BrCF2(CF2) n CF2Br (n = 2, 4, 6), and 1,4-diazabicyclo[2.2.2]octane (DABCO). Single-crystal X-ray diffraction studies of the colourless crystals identified 1,4-diazabicyclo[2.2.2]octane–1,4-dibromoperfluorobutane (1/1), C4Br2F8·C6H12N2, (I), 1,4-diazabicyclo[2.2.2]octane–1,6-dibromoperfluorohexane (1/1), C6Br2F12·C6H12N2, (II), and 1,4-diazabicyclo[2.2.2]octane–1,8-dibromoperfluorooctane (1/1), C8Br2F16·C6H12N2, (III), each of which displays a one-dimensional halogen-bonded network. All three adducts exhibit N...Br distances less than the sum of the van der Waals radii, with butane analogue (I) showing the shortest N...Br halogen-bond distances yet reported between a bromoperfluorocarbon and a nitrogen base [2.809 (3) and 2.818 (3) Å], which are 0.58 and 0.59 Å shorter than the sum of the van der Waals radii.
Acta Crystallographica Section C Structural Chemistry, Volume 73, pp 862-868; https://doi.org/10.1107/s2053229617013481

Abstract:
Pyrimidines are important compounds in biology and medicine, and the aminopyrimidine fragment can be identified in three of the four bases in DNA. The targeted drug action of pharmaceuticals containing this functionality is likely to depend heavily on molecular recognition processes involving hydrogen bonding. Crystallization of an equimolar mixture of 4-amino-5-chloro-2,6-dimethylpyrimidine and 5-chloro-2-hydroxybenzoic acid yielded two forms of the 1:1 salt, C6H9ClN3+·C7H4ClO3, each containing a different tautomeric form of the cation. 6-Amino-5-chloro-2,4-dimethylpyrimidin-1-ium 5-chloro-2-hydroxybenzoate, (I), crystallizes in the space group P\overline{1}, with Z′ = 2, and all of the component ions are fully ordered. 4-Amino-5-chloro-2,6-dimethylpyrimidin-1-ium 5-chloro-2-hydroxybenzoate, (II), also crystallizes with Z′ = 2, but in the space group P21/c and as a merohedral twin which closely mimics an orthorhombic unit cell. In (II), one of the cations and one of the anions is disordered, each over two sets of atomic sites having occupancies of 0.836 (2) and 0.164 (2), and 0.834 (2) and 0.166 (2). The bond lengths in the cations of (I) and (II) provide evidence for o-quinonoid and p-quinonoid bond fixation, respectively. A combination of six N—H...O hydrogen bonds links the component ions of (I) into two independent four-ion aggregates, but the ions in (II) are linked by a combination of four N—H...O and two N—H...N hydrogen bonds to form a three-dimensional framework structure. The recently reported structure of 2-amino-4,6-dimethoxypyrimidin-1-ium thiophene-2-carboxylate, C6H10N3O2+·C5H3O2S, (III), has been rerefined, using the original data set, to show that the anion is disordered over two sets of atomic sites, approximately related by a 180° rotation about the exocyclic C—C bond, and having occupancies of 0.8687 (19) and 0.1313 (19).
Yi-Xuan Hou, Dong Liu
Acta Crystallographica Section C Structural Chemistry, Volume 73, pp 869-873; https://doi.org/10.1107/s2053229617013560

Abstract:
In the development of coordination-driven crystalline materials, O- and N-atom donors from carboxylate and pyridyl-based ligands are widely used classes of multidentate bridging ligands composed of several terminal coordinating groups linked by either rigid or flexible spacers. The rigidity of the ligands can play a vital role in the determination of the structures formed. A new CdII supramolecular compound, namely poly[μ-adipato-κ2O1:O4-μ-adipato-κ4O1,O1′:O4,O4′-diaquabis[μ-1,4-bis(pyridin-4-yl)-1,3-butadiene-κ2N:N′]dicadmium(II)], [Cd2(C6H8O4)2(C14H12N2)2(H2O)2] n , (I), has been synthesized by the self-assembly of Cd(NO3)2·4H2O, adipic acid (hexane-1,6-dioic acid; H2adp) and the dipyridyl ligand 1,4-bis(pyridin-4-yl)buta-1,3-diene (1,4-bpbd) under hydrothermal conditions. Single-crystal X-ray diffraction analysis reveals that each CdII centre is located in a distorted octahedral coordination environment, coordinated by one water O atom, three carboxylate O atoms from two different adp2− ligands and two N atoms from two different 1,4-bpbd ligands. The Cd(H2O) units are interconnected by the μ22-adp2−, μ24-adp2− and 1,4-bpbd ligands, which lie across centres of inversion, to give a 66-dia network. Large cavities within a single diamondoid network permit the mutual threefold interpenetration of crystallographically equivalent frameworks. Hydrogen-bonding interactions between the coordinated water molecules and adp2− carboxylate O atoms anchor the interpenetrating networks into a unique three-dimensional supramolecular structure. Topologically, taking the coordinated water molecules and CdII centres as nodes, the whole architecture can be simplified as a binodal (3,7)-connected supramolecular framework. The identity of (I) was further characterized by IR spectroscopy, elemental analysis, thermogravimetric analysis and powder X-ray diffraction. The solid-state photoluminescence properties of (I) were also investigated.
Abstract:
In the title compound, C13H9ClN2O5, the dihedral angle between the planes of the benzene and pyridine rings is 55.30 (13)°. The nitro group is tilted by 38.21 (10)° with respect to the mean plane of the pyridine ring. In the crystal, molecules are linked by O—H...O and C—H...O hydrogen bonds, forming a three-dimensional framework. The crystal packing is further stabilized by π–π stacking interactions [intercentroid distance = 3.5877 (17) Å].
, Matthew R. DeStefano, Robert A. Lewis
Acta Crystallographica Section E Crystallographic Communications, Volume 73, pp 1616-1621; https://doi.org/10.1107/s2056989017014232

Abstract:
Copper(II) complexes of benzimidazole are known to exhibit biological activity that makes them of interest for chemotherapeutic and other pharmaceutical uses. The complex bis(acetato-κO){5,6-dimethyl-2-(pyridin-2-yl)-1-[(pyridin-2-yl)methyl]-1H-benzimidazole-κ2N2,N3}copper(II), has been prepared. The absorption spectrum has features attributed to intraligand and ligand-field transitions and the complex exhibits ligand-centered room-temperature luminescence in solution. The acetonitrile monosolvate, [Cu(C2H3O2)2(C20H18N4)]·C2H3N (1), and the ethanol hemisolvate, [Cu(C2H3O2)2(C20H18N4)]·0.5C2H6O (2), have been structurally characterized. Compound2has two copper(II) complexes in the asymmetric unit. In both1and2, distorted square-planar N2O2coordination geometries are observed and the Cu—N(Im) bond distance is slightly shorter than the Cu—N(py) bond distance. Intermolecular π–π interactions are found in1and2. A weak C—H...π interaction is observed in1.
, Katrina Tait, William Tam
Abstract:
In the title compound, C10H17NO3, the five-membered ring is in a slightly twisted envelope conformation. The carbonyl group is disordered over two sites on the five-membered ring, with refined occupancies of 0.906 (4) and 0.094 (4). In the crystal, molecules are linkedviaN—H...O hydrogen bonds formingC(4) chains along [001].
, Katrina Tait, Alysia Horvath, William Tam
Abstract:
In the title compound, C15H27NO4, the cyclopentane ring adopts an envelope conformation with the methylene group as the flap. The dihedral angle between the cyclopropane ring and the cyclopentane ring (all atoms) is 77.54 (13)°. In the crystal, molecules are linkedviaO—H...O hydrogen bonds, formingC(7) chains propagating along [010].
Delia Bautista, Sergio J. Benitez-Benitez
Acta Crystallographica Section E Crystallographic Communications, Volume 73, pp 1612-1615; https://doi.org/10.1107/s2056989017014281

Abstract:
The binuclear title complex, di-μ-iodido-bis({2-[(benzylamino-κN)methyl]phenyl-κC1}palladium(II)), [Pd2I2(C14H14N)2], was prepared by reaction of [Pd{C6H4(CH2NHCH2Ph)-2}(μ-OAc)]2with NaI. It crystallizes with one discrete molecule in the asymmetric unit. The molecule presents an iodide-bridged dimeric structure with acisoidarrangement with respect to theC,N-cyclopalladated ligands. Both PdIIatoms have a slightly distorted square-planar coordination environment. Weak intermolecular contacts of the type C—H...Pd seem to have a significant influence on the arrangement of the molecules along thebaxis in the crystal.
Acta Crystallographica Section E Crystallographic Communications, Volume 73, pp 1607-1611; https://doi.org/10.1107/s2056989017014128

Abstract:
The title compound, C23H21N3O2, is constructed about an almost planar disubstituted aminourea residue (r.m.s. deviation = 0.0201 Å), which features an intramolecular amine-N—H...N(imine) hydrogen bond. In the `all-trans' chain connecting this to the terminal methoxybenzene residue, the conformation about each of the imine and ethylene double bonds isE. In the crystal, amide-N—H...O(carbonyl) hydrogen bonds connect centrosymmetrically related molecules into dimeric aggregates, which also incorporate ethylene-C—H...O(amide) interactions. The dimers are linked by amine–phenyl-C—H...π(imine–phenyl) and methoxybenzene-C—H...π(amine–phenyl) interactions to generate a three-dimensional network. The importance of C—H...π interactions in the molecular packing is reflected in the relatively high contributions made by C...H/H...C contacts to the Hirshfeld surface,i.e. 31.6%.
Lucia Piñeiro-López, Francisco Javier Valverde Muñoz, ,
Abstract:
The molecular structure of the title compound, [FePt(CN)4(C14H8N2)2(H2O)2]n, consists of one-dimensional polymeric [–Fe–NC–Pt(CN)2–CN–]chains. Two water molecules and two monodentate 1,4-bis(pyridin-4-yl)buta-1,3-diyne (bpb) ligand molecules complete the octahedral coordination sphere of the FeIIatoms. The Fe—N(py) bond length (py is pyridine) is 2.2700 (15) Å, Fe—N(cyanide) is 2.1185 (16) Å and the Fe—O distance is 2.1275 (14) Å. The water molecules are hydrogen bonded to either bpb ligands or cyanide groups of the planar [Pt(CN)4]2−anion of adjacent polymeric chains. These O—H...N hydrogen bonds, in conjunction with offset and tilted π–π stacking interactions between bpb ligands and cyanide groups, extend the one-dimensional chains into a three-dimensional assembly.
Acta Crystallographica Section E Crystallographic Communications, Volume 73, pp 1603-1606; https://doi.org/10.1107/s2056989017013391

Abstract:
The title compound, C31H48O6, is a polyoxygenated epoxy steroid obtained by a multi-step synthesis involving oxidation of 7-dehydrocholesterol. It crystallizes in theP212121space group; however, the absolute structure of the molecule in the crystal could not be determined by resonant scattering. The configuration at the C5 and C6 positions is in both cases of the α-type, as is that of the C atoms of the epoxy ring. Molecules in the crystal form chains parallel to thebaxis by hydrogen bonding between O—H donors and carbonyl O-atom acceptors. Some atoms of the alkyl chain are disordered over two orientations, with a refined occupancy ratio of 0.511 (10):0.489 (10).
, Emily Carlson,
Abstract:
The relative stereochemistry of the title compound, C17H24O2, has been confirmed by the X-ray analysis. The seven-membered ring is in a pseudo-boat conformation with both methoxy substituents in equatorial sites.
Alexander Anis’Kov, Vyacheslav Grinev, Irina Klochkova
Acta Crystallographica Section E Crystallographic Communications, Volume 73, pp 1622-1625; https://doi.org/10.1107/s2056989017014165

Abstract:
The synthesis and crystal structure of the title compound, C28H28O2, are reported. The C=C—C—C torsion angles in the phenylmethylidene units are 166.6 (3) and −48.0 (4)°. In the crystal, molecules form a three-dimensional network by means of weak C—H...O hydrogen bonds. The most important contributions to the crystal structure are the H...H interactions (68.8%), while the H...O contacts account for 4.5%.
Abstract:
In the title compound, C19H16N4, the pyrazolopyrimidine unit is slightly twisted. A combination of π-stacking and offset π-stacking interactions forms columns along theb-axis direction.
Abstract:
The title compound, C7H6Br2N2O, was obtained from a condensation reaction of 3,5-dibromo-2-hydroxybenzaldehyde and hydrazine hydrate. The molecule is approximately planar, the largest deviation from the mean plane through all of the non-H atoms being 0.053 (1) Å. The molecular conformation is stabilized by an intramolecular O—H...N hydrogen bond, generating anS(6) ring motif. In the crystal, intermolecular N—H...Br and N—H...O hydrogen bonds link the molecules, forming chains parallel to thebaxis. Molecules are further linked by π–π stacking interactions, with centroid–centroid distances of 3.925 (3)–3.926 (3) Å, forming a three-dimensional network.
Błażej Dziuk, , Krzysztof Ejsmont, Zdzisław Daszkiewicz
Abstract:
There is one independent molecule in the asymmetric unit of the title compound (alternatively namedN-hydroxyacetamide), C2H5NO2. It crystallizes in the noncentrosymmetric space groupP43. The structure is an anhydrous form of acetylhydroxamic acid with typical geometry that corresponds well with the hydrated structure described by Bracher & Small [Acta Cryst.(1970), B26, 1705–1709]. In the crystal, N—H...O and O—H...O hydrogen bonds connect the molecules into chains in thec-axis direction.
Abstract:
In the title compound, C18H17ClN4O2, the dihydroquinoxaline moiety deviates slightly from planarity. The benzene ring and its chloro and methylene substituents are disordered over two sets of sites, with an occupancy ratio of 0.675 (3):0.325 (3). In the crystal, corrugated sheets parallel to (100) are formed by N—H...O, N—H...Cl and N—H...N hydrogen bonds. The structure was refined as a two-component inversion twin.
Abstract:
In the title compound, [Ir(C8H12)(C8H14N2)(C18H15P)]BF4, the cationic complex has the anticipated square-planar geometry. The asymmetric unit comprises the iridium complex and one tetrafluoridoborate anion. The space group is non-centrosymmetric, with the Flack parameter of 0.007 (3) well determined, and confirms the hand for the complex cation. This compound shows promising catalytic activity in transfer hydrogenation reactions.
, Ming-Fu Lin, Daniel S. Damiani, William F. Schlotter, Joshua J. Turner, Dennis Nordlund, Hirohito Ogasawara
Journal of Synchrotron Radiation, Volume 24, pp 1180-1186; https://doi.org/10.1107/s1600577517011869

Abstract:
A method for measuring resonant inelastic X-ray scattering based on the conversion of X-ray photons into photoelectrons is presented. The setup is compact, relies on commercially available detectors, and offers significant flexibility. This method is demonstrated at the Linac Coherent Light Source with ∼0.5 eV resolution at the cobaltL3-edge, with signal rates comparable with traditional grating spectrometers.
, Karl F. Ludwig
Journal of Synchrotron Radiation, Volume 24, pp 1187-1194; https://doi.org/10.1107/s1600577517011924

Abstract:
The recent development of surface growth studies using X-ray photon correlation spectroscopy in a grazing-incidence small-angle X-ray scattering (Co-GISAXS) geometry enables the investigation of dynamical processes during kinetic roughening in greater detail than was previously possible. In order to investigate the Co-GISAXS behavior expected from existing growth models, calculations and (2+1)-dimension simulations of linear Kuramoto–Sivashinsky and non-linear Kardar–Parisi–Zhang surface growth equations are presented which analyze the temporal correlation functions of the height–height structure factor. Calculations of the GISAXS intensity auto-correlation functions are also performed within the Born/distorted-wave Born approximation for comparison with the scaling behavior of the height–height structure factor and its correlation functions.
Matimon Sangsawang, Kittipong Chainok, Nanthawat Wannarit
Acta Crystallographica Section E Crystallographic Communications, Volume 73, pp 1599-1602; https://doi.org/10.1107/s2056989017013871

Abstract:
The title compound, [CdNa2(C8H4O4)2(C3H7NO)(H2O)2]nor [CdNa2(1,3-bdc)2(DMF)(H2O)2]n, is a new CdII–NaIheterobimetallic coordination polymer. The asymmetric unit consists of one CdIIatom, two NaIatoms, two 1,3-bdc ligands, two coordinated water molecules and one coordinated DMF molecule. The CdIIatom exhibits a seven-coordinate geometry, while the NaIatoms can be considered to be pentacoordinate. The metal ions and their symmetry-related equivalents are connectedviachelating–bridging carboxylate groups of the 1,3-bdc ligands to generate a three-dimensional framework. In the crystal, there are classical O—H...O hydrogen bonds involving the coordinated water molecules and the 1,3-bdc carboxylate groups and π–π stacking between the benzene rings of the 1,3-bdc ligands present within the frameworks.
Acta Crystallographica Section F Structural Biology Communications, Volume 73, pp 560-567; https://doi.org/10.1107/s2053230x17013280

Abstract:
ATG16L1 plays a major role in autophagy. It acts as a molecular scaffold which mediates protein–protein interactions essential for autophagosome formation. The ATG12~ATG5–ATG16L1 complex is one of the key complexes involved in autophagosome formation. Human ATG16L1 comprises 607 amino acids with three functional domains named ATG5BD, CCD and WD40, where the C-terminal WD40 domain represents approximately 50% of the full-length protein. Previously, structures of the C-terminal WD40 domain of human ATG16L1 as well as of human ATG12~ATG5 in complex with the ATG5BD of ATG16L1 have been reported. However, apart from the ATG5BD, no structural information for the N-terminal half, including the CCD, of human ATG16L1 is available. In this study, the authors aimed to structurally characterize the N-terminal half of ATG16L1. ATG16L111–307 in complex with ATG5 has been purified and crystallized in two crystal forms. However, both crystal structures revealed degradation of ATG16L1, resulting in crystals comprising only full-length ATG5 and the ATG5BD of ATG16L1. The structures of ATG5–ATG5BD in two novel crystal forms are presented, further supporting the previously observed dimerization of ATG5–ATG16L1. The reported degradation points towards a high instability at the linker region between the ATG5BD and the CCD in ATG16L1. Based on this observation and further biochemical analysis of ATG16L1, a stable 236-amino-acid subfragment comprising residues 72–307 of the N-terminal half of ATG16L1, covering the residual, so far structurally uncharacterized region of human ATG16L1, was identified. Here, the identification, purification, biochemical characterization and crystallization of the proteolytically stable ATG16L172–307 subfragment are reported.
Acta Crystallographica Section F Structural Biology Communications, Volume 73, pp 579-587; https://doi.org/10.1107/S2053230X17013838

Abstract:
The first crystal structures of the class D β-lactamases OXA-181 and OXA-245 were determined to 2.05 and 2.20 Å resolution, respectively; in addition, the structure of a new crystal form of OXA-163 was resolved to 2.07 Å resolution. All of these enzymes are OXA-48-like and have been isolated from different clinicalKlebsiella pneumoniaestrains and also from other human pathogens such asPseudomonas aeruginosaandEscherichia coli. Here, enzyme kinetics and thermostability studies are presented, and the new crystal structures are used to explain the observed variations. OXA-245 had the highest melting point (Tm= 55.8°C), as determined by differential scanning calorimetry, compared with OXA-163 (Tm= 49.4°C) and OXA-181 (Tm= 52.6°C). The differences could be explained by the loss of two salt bridges in OXA-163, and an overall decrease in the polarity of the surface of OXA-181 compared with OXA-245.
, Jane S. Richardson, David C. Richardson
Acta Crystallographica Section D Structural Biology, Volume 73, pp 852-859; https://doi.org/10.1107/s2059798317013729

Abstract:
Hoogsteen base pairs are seen in DNA crystal structures, but only rarely. This study tests whether Hoogsteens or othersynpurines are either under-modeled or over-modeled, which are known problems for rare conformations. Candidate purines needing asyn/anti180° flip were identified by diagnostic patterns of difference electron-density peaks. Manual inspection narrowed 105 flip candidates to 20 convincing cases, all at ≤2.7 Å resolution. Rebuilding and refinement confirmed that 14 of these were authentic purine flips. Seven examples are modeled as Watson–Crick base pairs but should be Hoogsteens (commonest at duplex termini), and three had the opposite issue.Syn/antiflips were also needed for some single-stranded purines. Five of the 20 convincing cases arose from an unmodeled alternate duplex running in the opposite direction. These are in semi-palindromic DNA sequences bound by a homodimeric protein and show flipped-purine-like difference peaks at residues where the palindrome is imperfect. This study documents types of incorrect modeling which are worth avoiding. However, the primary conclusions are that such mistakes are infrequent, the bias towards fittingantipurines is very slight, and the occurrence rate of Hoogsteen base pairs in DNA crystal structures remains unchanged from earlier estimates at ∼0.3%.
Acta Crystallographica Section F Structural Biology Communications, Volume 73, pp 568-573; https://doi.org/10.1107/s2053230x17013759

Abstract:
Norovirusis a major causative pathogen of nonbacterial acute gastroenteritis. Despite the sequence similarity among various strains, noroviruses of different genotypes show different antigenicities and different binding profiles to histo-blood group antigens (HBGAs). To reveal the relationships between the structure of the capsid and the diversity in antigenicity and the HBGA-binding profile, virus-like particles (VLPs) of the Chiba strain that belongs to genogroup I, genotype 4 were crystallized for X-ray structural analysis. Diffraction data were collected and processed at 3.2 Å resolution. The crystal belonged to space groupI222, with unit-cell parametersa= 290.0,b= 310.4c= 350.4 Å. The possible packing model indicated that the diameter of the particle was 280 Å, which was much smaller than the 38 nm VLPs ofNorovirusNorwalk strain (NV) withT= 3 icosahedral symmetry and composed of 180 VP1 proteins. The structure was solved by molecular replacement using the structure of the VP1 pentamer of NV 38 nm VLPs as a search model, revealing that the VLPs were smaller particles: 23 nm VLPs withT= 1 icosahedral symmetry, the structure of which has not yet been analyzed at high resolution. The structure of 23 nm VLPs will enable the two different VLPs ofNorovirusto be compared, which will provide important information for understanding the structural basis of capsid formation.
Acta Crystallographica Section F Structural Biology Communications, Volume 73, pp 574-578; https://doi.org/10.1107/s2053230x17013826

Abstract:
A microfluidic platform was used to address the problems of obtaining diffraction-quality crystals and crystal handling during transfer to the X-ray diffractometer. Crystallization conditions of a protein of pharmaceutical interest were optimized and X-ray data were collected both in situ and ex situ.
Abdullah Sirindil, Marianne Quiquandon,
Acta Crystallographica Section A Foundations and Advances, Volume 73, pp 427-437; https://doi.org/10.1107/s2053273317013882

Abstract:
An analysis is presented of the new types of defects that can appear in crystalline structures where the positions of the atoms and the unit cell belong to the same {\bb Z}-module,i.e.are irrational projections of anN> 3-dimensional (N-D) lattice Λ as in the case of quasicrystals. Beyond coherent irrationally oriented twins already discussed in a previous paper [Quiquandonet al.(2016).Acta Cryst.A72, 55–61], new two-dimensional translational defects are expected, the translation vectors of which, being projections of nodes of Λ, have irrational coordinates with respect to the unit-cell reference frame. Partial dislocations, called heremodule dislocations, are the linear defects bounding these translation faults. A specific case arises when the Burgers vectorBis the projection of a non-zero vector of Λ that is perpendicular to the physical space. This new kind of dislocation is called ascalar dislocationsince, because its Burgers vector in physical space is zero, it generates no displacement field and has no interaction with external stress fields and other dislocations.
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